Abstract
BackgroundThe σ54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown.ResultsTo characterize the σ54-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ54-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ54 regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ54-dependent regulators.ConclusionsThe σ54-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ54-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2176-y) contains supplementary material, which is available to authorized users.
Highlights
The σ54 subunit controls a unique class of promoters in bacteria
We inferred several σ54-dependent regulons not known before
In order to characterize a particular type of transcriptional regulation in bacteria, one needs to elucidate all the necessary components in this process, which typically are: transcriptional regulator, its binding sites, and a set of regulated genes or operons
Summary
The σ54 subunit controls a unique class of promoters in bacteria Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. One of the sigma factors, called alternative sigma factor σ54, significantly differs from all other known sigma factor proteins in two respects (reviewed in [1]) It recognizes and binds characteristic promoters with GG −24 and TGC −12 elements that are more conserved than the promoters of σ70 family. Σ54 strictly requires the ATP hydrolysis activity of an activating transcription factor (TF) for the oligomer requires DNA looping between the UAS and promoter This looping is often facilitated by bacterial chromatin proteins like integration host factor or histonelike protein HU. Initiation of σ54-dependent transcription involves promoter binding by σ54-containing
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